arXiv subjects

Jan Janssen

Publications and source records attributed to Jan Janssen.

12 recordsLinked to original sources

arXiv2026

Surrogate-Gated Generation and Foundation-Model Embeddings for Bayesian Materials Design

Closed-loop materials discovery iterates between proposing candidate structures and evaluating their properties, and property evaluation dominates the cost. In the generative variant, a learned prior proposes candidate crystals and a property oracle scores them; we ask whether a cheap probabilistic surrogate can triage the generator's output, and what such a surrogate must do well. Across three architecturally distinct pretrained diffusion priors (MatterGen, CrystalFlow, ADiT) and two targets (room-temperature heat capacity and bulk modulus), we insert a Gaussian process acquisition gate between structure generation and the oracle in an RL-steered generative workflow. The gate matches or exceeds ungated fine-tuning of the generative model while capping oracle calls at a fixed per-cycle budget. Budget-matched ablations isolate the mechanism. At an identical four-call budget, ranking-based selection outperforms arbitrary selection, confirming that the gain comes from the surrogate's choice; the gate comes within $\sim$9\% of exhaustive oracle spending at roughly one-fifth of the calls. A density-functional-theory check of the bulk-modulus discoveries confirms the learned oracle to within 2.5\% on average and the surrogate's ranking of the generated structures at Spearman $\rho = 0.94$. A cross-factorial benchmark of surrogate performance spanning mechanical, electronic, and vibrational properties identifies pretrained ORB embeddings with a Gaussian process as the most reliable combination, which we adopt as the building blocks of the proposed workflow. The complete pipeline is released as open-source software.

cond-mat.mtrl-sci↗

arXiv2025

Deep Gaussian Process-based Cost-Aware Batch Bayesian Optimization for Complex Materials Design Campaigns

The accelerating pace and expanding scope of materials discovery demand optimization frameworks that efficiently navigate vast, nonlinear design spaces while judiciously allocating limited evaluation resources. We present a cost-aware, batch Bayesian optimization scheme powered by deep Gaussian process (DGP) surrogates and a heterotopic querying strategy. Our DGP surrogate, formed by stacking GP layers, models complex hierarchical relationships among high-dimensional compositional features and captures correlations across multiple target properties, propagating uncertainty through successive layers. We integrate evaluation cost into an upper-confidence-bound acquisition extension, which, together with heterotopic querying, proposes small batches of candidates in parallel, balancing exploration of under-characterized regions with exploitation of high-mean, low-variance predictions across correlated properties. Applied to refractory high-entropy alloys for high-temperature applications, our framework converges to optimal formulations in fewer iterations with cost-aware queries than conventional GP-based BO, highlighting the value of deep, uncertainty-aware, cost-sensitive strategies in materials campaigns.

cond-mat.mtrl-sci↗

arXiv2025

DREAMS: Density Functional Theory Based Research Engine for Agentic Materials Simulation

Large language model (LLM) agents can execute long-horizon scientific workflows, but their numerical outputs are difficult to trust: agents lose context, game verification checks, and can produce large volumes of plausible yet invalid results. We introduce the DFT-based Research Engine for Agentic Materials Simulation (DREAMS), a hierarchical multi-agent framework for density functional theory (DFT) built around a multi-tier safety guard. The guard applies deterministic checks wherever explicit criteria exist and scoped LLM judgment elsewhere, evaluating one parameter at a time and tracing every value to its registered source. Verification extends from tool-call time, where fabricated, laundered, or unsourced values are rejected before entering the workflow, to report time, where a judge audits the full provenance graph behind every claim; a shared canvas preserves information integrity across hundreds of steps. DREAMS achieves average errors below 1% on the Sol27LC lattice-constant benchmark, reproduces expert-level adsorption-energy differences on the CO/Pt(111) puzzle, and quantifies functional-driven uncertainty with Bayesian ensemble sampling, confirming the face-centered-cubic (FCC) site preference at the generalized gradient approximation (GGA) level. Compared with its unguarded counterpart, which reached a nearly correct answer while only 81% of its essential steps succeeded, the guarded system verifies every essential step at approximately 13 times the input tokens; verification layers can be disabled individually to balance trustworthiness against cost, and the tuned judge rules transfer across five judge models. DREAMS operates at an enhanced L2 (L2+) automation level and demonstrates capabilities approaching L3 automation, providing a path toward trustworthy, high-throughput autonomous materials simulation.

cs.AI↗

arXiv2025

Accurate and Uncertainty-Aware Multi-Task Prediction of HEA Properties Using Prior-Guided Deep Gaussian Processes

Surrogate modeling techniques have become indispensable in accelerating the discovery and optimization of high-entropy alloys(HEAs), especially when integrating computational predictions with sparse experimental observations. This study systematically evaluates the fitting performance of four prominent surrogate models conventional Gaussian Processes(cGP), Deep Gaussian Processes(DGP), encoder-decoder neural networks for multi-output regression and XGBoost applied to a hybrid dataset of experimental and computational properties in the AlCoCrCuFeMnNiV HEA system. We specifically assess their capabilities in predicting correlated material properties, including yield strength, hardness, modulus, ultimate tensile strength, elongation, and average hardness under dynamic and quasi-static conditions, alongside auxiliary computational properties. The comparison highlights the strengths of hierarchical and deep modeling approaches in handling heteroscedastic, heterotopic, and incomplete data commonly encountered in materials informatics. Our findings illustrate that DGP infused with machine learning-based prior outperform other surrogates by effectively capturing inter-property correlations and input-dependent uncertainty. This enhanced predictive accuracy positions advanced surrogate models as powerful tools for robust and data-efficient materials design.

cs.LG↗

arXiv2025

Application-specific machine-learned interatomic potentials: exploring the trade-off between DFT convergence, MLIP expressivity, and computational cost

Machine-learned interatomic potentials (MLIPs) are revolutionizing computational materials science and chemistry by offering an efficient alternative to {\em ab initio} molecular dynamics (MD) simulations. However, fitting high-quality MLIPs remains a challenging, time-consuming, and computationally intensive task where numerous trade-offs have to be considered, e.g., How much and what kind of atomic configurations should be included in the training set? Which level of {\em ab initio} convergence should be used to generate the training set? Which loss function should be used for fitting the MLIP? Which machine learning architecture should be used to train the MLIP? The answers to these questions significantly impact both the computational cost of MLIP training and the accuracy and computational cost of subsequent MLIP MD simulations. In this study, we use a configurationally diverse beryllium dataset and quadratic spectral neighbor analysis potential. We demonstrate that joint optimization of energy versus force weights, training set selection strategies, and convergence settings of the {\em ab initio} reference simulations, as well as model complexity can lead to a significant reduction in the overall computational cost associated with training and evaluating MLIPs. This opens the door to computationally efficient generation of high-quality MLIPs for a range of applications which demand different accuracy versus training and evaluation cost trade-offs.

physics.comp-ph↗

arXiv2025

A Python workflow definition for computational materials design

Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow exchange format to share workflows between Python-based WfMS, currently AiiDA, jobflow, and pyiron. This development is motivated by the similarity of these three Python-based WfMS, that represent the different workflow steps and data transferred between them as nodes and edges in a graph. With the PWD, we aim at fostering the interoperability and reproducibility between the different WfMS in the context of Findable, Accessible, Interoperable, Reusable (FAIR) workflows. To separate the scientific from the technical complexity, the PWD consists of three components: (1) a conda environment that specifies the software dependencies, (2) a Python module that contains the Python functions represented as nodes in the workflow graph, and (3) a workflow graph stored in the JavaScript Object Notation (JSON). The first version of the PWD supports directed acyclic graph (DAG)-based workflows. Thus, any DAG-based workflow defined in one of the three WfMS can be exported to the PWD and afterwards imported from the PWD to one of the other WfMS. After the import, the input parameters of the workflow can be adjusted and computing resources can be assigned to the workflow, before it is executed with the selected WfMS. This import from and export to the PWD is enabled by the PWD Python library that implements the PWD in AiiDA, jobflow, and pyiron.

cs.SE↗

arXiv2025

34 Examples of LLM Applications in Materials Science and Chemistry: Towards Automation, Assistants, Agents, and Accelerated Scientific Discovery

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 34 total projects developed during the second annual Large Language Model Hackathon for Applications in Materials Science and Chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

cs.LG↗

arXiv2024

Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows

The Workflows Community Summit gathered 111 participants from 18 countries to discuss emerging trends and challenges in scientific workflows, focusing on six key areas: time-sensitive workflows, AI-HPC convergence, multi-facility workflows, heterogeneous HPC environments, user experience, and FAIR computational workflows. The integration of AI and exascale computing has revolutionized scientific workflows, enabling higher-fidelity models and complex, time-sensitive processes, while introducing challenges in managing heterogeneous environments and multi-facility data dependencies. The rise of large language models is driving computational demands to zettaflop scales, necessitating modular, adaptable systems and cloud-service models to optimize resource utilization and ensure reproducibility. Multi-facility workflows present challenges in data movement, curation, and overcoming institutional silos, while diverse hardware architectures require integrating workflow considerations into early system design and developing standardized resource management tools. The summit emphasized improving user experience in workflow systems and ensuring FAIR workflows to enhance collaboration and accelerate scientific discovery. Key recommendations include developing standardized metrics for time-sensitive workflows, creating frameworks for cloud-HPC integration, implementing distributed-by-design workflow modeling, establishing multi-facility authentication protocols, and accelerating AI integration in HPC workflow management. The summit also called for comprehensive workflow benchmarks, workflow-specific UX principles, and a FAIR workflow maturity model, highlighting the need for continued collaboration in addressing the complex challenges posed by the convergence of AI, HPC, and multi-facility research environments.

cs.DC↗

arXiv2024

Hierarchical Gaussian Process-Based Bayesian Optimization for Materials Discovery in High Entropy Alloy Spaces

Bayesian optimization (BO) is a powerful and data-efficient method for iterative materials discovery and design, particularly valuable when prior knowledge is limited, underlying functional relationships are complex or unknown, and the cost of querying the materials space is significant. Traditional BO methodologies typically utilize conventional Gaussian Processes (cGPs) to model the relationships between material inputs and properties, as well as correlations within the input space. However, cGP-BO approaches often fall short in multi-objective optimization scenarios, where they are unable to fully exploit correlations between distinct material properties. Leveraging these correlations can significantly enhance the discovery process, as information about one property can inform and improve predictions about others. This study addresses this limitation by employing advanced kernel structures to capture and model multi-dimensional property correlations through multi-task (MTGPs) or deep Gaussian Processes (DGPs), thus accelerating the discovery process. We demonstrate the effectiveness of MTGP-BO and DGP-BO in rapidly and robustly solving complex materials design challenges that occur within the context of complex multi-objective optimization -- carried out by leveraging the pyiron workflow manager over FCC FeCrNiCoCu high entropy alloy (HEA) spaces, where traditional cGP-BO approaches fail. Furthermore, we highlight how the differential costs associated with querying various material properties can be strategically leveraged to make the materials discovery process more cost-efficient.

cond-mat.mtrl-sci↗

arXiv2024

From electrons to phase diagrams with classical and machine learning potentials: automated workflows for materials science with pyiron

We present a comprehensive and user-friendly framework built upon the pyiron integrated development environment (IDE), enabling researchers to perform the entire Machine Learning Potential (MLP) development cycle consisting of (i) creating systematic DFT databases, (ii) fitting the Density Functional Theory (DFT) data to empirical potentials or MLPs, and (iii) validating the potentials in a largely automatic approach. The power and performance of this framework are demonstrated for three conceptually very different classes of interatomic potentials: an empirical potential (embedded atom method - EAM), neural networks (high-dimensional neural network potentials - HDNNP) and expansions in basis sets (atomic cluster expansion - ACE). As an advanced example for validation and application, we show the computation of a binary composition-temperature phase diagram for Al-Li, a technologically important lightweight alloy system with applications in the aerospace industry.

cond-mat.mtrl-sci↗

arXiv2022

Computationally accelerated experimental materials characterization -- drawing inspiration from high-throughput simulation workflows

Computational materials science increasingly benefits from data management, automation, and algorithm-based decision-making for the simulation of material properties and behavior. Experimental materials science also changes rapidly by incorporation of `machine learning' in materials discovery campaigns. The obvious benefits which include automation, reproducibility, data provenance, and reusability of managed data, however, is not widely available in the experimental domain. We present an implementation of a Active Learning loop with a direct interface to an experimental measurement device in pyiron, a framework designed for high-throughput simulations, as demonstrator how to combine experimental and simulated data in one framework. Apart from the acceleration provided by the active learning approach, additional acceleration of the experimental characterization is achieved by using prior knowledge from density functional theory simulations as well as composition-property predictions from literature mining using correlations in word embeddings. With data from all domains in the same framework, a heretofore untapped and much-needed potential for the acceleration of materials characterization and materials discovery campaigns becomes available.

cond-mat.mtrl-sci↗

arXiv2021

Automated optimization of convergence parameters in plane wave density functional theory calculations via a tensor decomposition-based uncertainty quantification

First principles approaches have revolutionized our ability in using computers to predict, explore and design materials. A major advantage commonly associated with these approaches is that they are fully parameter free. However, numerically solving the underlying equations requires to choose a set of convergence parameters. With the advent of high-throughput calculations it becomes exceedingly important to achieve a truly parameter free approach. Utilizing uncertainty quantification (UQ) and tensor decomposition we derive a numerically highly efficient representation of the statistical and systematic error in the multidimensional space of the convergence parameters. Based on this formalism we implement a fully automated approach that requires as input the target accuracy rather than convergence parameters. The performance and robustness of the approach are shown by applying it to a large set of elements crystallizing in a cubic fcc lattice.

cond-mat.mtrl-sci↗